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- PDB-4j3g: Crystal structure of Ribosomal-protein-alanine N-acetyltransferas... -

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Basic information

Entry
Database: PDB / ID: 4j3g
TitleCrystal structure of Ribosomal-protein-alanine N-acetyltransferase from Brucella melitensis
ComponentsGCN5-related N-acetyltransferase
KeywordsTRANSFERASE / SSGCID / Seattle Structural Genomics Center for Infectious Disease / Ribosomal-protein-alanine N-acetyltransferase
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / metal ion binding
Similarity search - Function
Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / GCN5-related N-acetyltransferase
Similarity search - Component
Biological speciesBrucella melitensis biovar Abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Ribosomal-protein-alanine N-acetyltransferase from Brucella melitensis
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Sankaran, B. / Fairman, J.W. / Lorimer, D. / Edwards, T.E.
History
DepositionFeb 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GCN5-related N-acetyltransferase
B: GCN5-related N-acetyltransferase
C: GCN5-related N-acetyltransferase
D: GCN5-related N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,50917
Polymers82,5694
Non-polymers94013
Water9,926551
1
A: GCN5-related N-acetyltransferase
B: GCN5-related N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7208
Polymers41,2852
Non-polymers4356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-50 kcal/mol
Surface area15090 Å2
MethodPISA
2
C: GCN5-related N-acetyltransferase
D: GCN5-related N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7899
Polymers41,2852
Non-polymers5047
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-49 kcal/mol
Surface area14970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.110, 57.000, 73.420
Angle α, β, γ (deg.)86.550, 88.150, 88.760
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
GCN5-related N-acetyltransferase


Mass: 20642.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biovar Abortus (bacteria)
Strain: 2308 / Gene: BAB1_1664 / Plasmid: BrabA.17352.a.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2YRK4, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 5 types, 564 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.79 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytics MCSG1, 200mM ammoinum sulfate, 100mM HEPES/NaOH pH 7.5, 25% PEG 3350, BrabA.17352.a.A1.PS01094 at 20mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 19, 2012
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 63809 / Num. obs: 62171 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 25.624 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.27
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.75-1.80.4572.81180754563196
1.8-1.840.3793.46174914428196
1.84-1.90.2874.56169394289196.4
1.9-1.960.2275.72167834251196.6
1.96-2.020.1787.21158214009196.7
2.02-2.090.1468.73156093962197
2.09-2.170.11610.74151763851197.2
2.17-2.260.09612.88141803610197.1
2.26-2.360.08314.82140883581197.8
2.36-2.470.07416.34133193394197.7
2.47-2.610.06618.04126923234197.9
2.61-2.770.05521.7118613030198.2
2.77-2.960.04824.46113032897198.5
2.96-3.20.03929.07104342705198.4
3.2-3.50.03434.3494882477198.7
3.5-3.910.0338.1884712240198.6
3.91-4.520.02840.2972431963198.9
4.52-5.530.02741.9866231679199.5
5.53-7.830.02940.851031302199.6
7.83-500.02746.022717706199.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.61 Å
Translation3.5 Å19.61 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
BOSdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2J8M

2j8m


Resolution: 1.75→46.32 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2033 / WRfactor Rwork: 0.1648 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8664 / SU B: 5.011 / SU ML: 0.082 / SU R Cruickshank DPI: 0.1223 / SU Rfree: 0.1187 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2119 3139 5 %RANDOM
Rwork0.1706 ---
all0.1727 63809 --
obs0.1727 62171 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.97 Å2 / Biso mean: 21.7738 Å2 / Biso min: 9.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å2-0.63 Å20.66 Å2
2--0.39 Å2-0.79 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5043 0 53 551 5647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195298
X-RAY DIFFRACTIONr_bond_other_d0.0010.025058
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.9577207
X-RAY DIFFRACTIONr_angle_other_deg0.711311533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2535681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46623.591259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30615856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8751546
X-RAY DIFFRACTIONr_chiral_restr0.0890.2805
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026151
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021299
X-RAY DIFFRACTIONr_mcbond_it1.1771.3712643
X-RAY DIFFRACTIONr_mcbond_other1.1761.3712642
X-RAY DIFFRACTIONr_mcangle_it1.8382.0513306
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 230 -
Rwork0.228 4322 -
all-4552 -
obs-4322 95.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8274-0.3362-0.04031.02090.45420.36640.06290.0916-0.0897-0.1354-0.07010.0508-0.1096-0.02270.00720.06930.01090.0040.0321-0.00660.01467.00228.46728.85
20.5542-0.0627-0.03850.7841-0.05120.49090.0020.02040.0219-0.0930.0755-0.0340.00420.0713-0.07760.0377-0.03150.01730.0548-0.02160.0223-7.69756.05761.392
30.6257-0.12540.10071.1027-0.33580.66470.0539-0.03-0.03310.1535-0.0132-0.0204-0.11020.0267-0.04070.0716-0.02890.00260.0183-0.00420.007310.85429.25757.885
40.9030.0375-0.43720.79710.55140.8594-0.0436-0.11690.06950.0970.07850.00450.09280.1163-0.03490.02680.0185-0.00910.0636-0.00850.0082-12.03256.4290.297
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 164
2X-RAY DIFFRACTION1A201 - 203
3X-RAY DIFFRACTION2C3 - 164
4X-RAY DIFFRACTION2C201 - 203
5X-RAY DIFFRACTION3B1 - 164
6X-RAY DIFFRACTION3B201 - 203
7X-RAY DIFFRACTION4D2 - 164
8X-RAY DIFFRACTION4D201 - 203

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